MolNFT v1 · #141120 · protein + DNA
Crystal structure of TREX1 in complex with a Y structured DNA
5YWS · Three-prime repair exonuclease 1: “Crystal structure of TREX1 in complex with a Y structured DNA”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.64). MolNFT v1 #141120 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YWS
- Type
- protein + DNA
- Length
- 502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three-prime repair exonuclease 1; A stem loop DNA with Y-structural terminal
- EC
- 3.1.11.2
- UniProt
- Q91XB0
- Ligands
- MG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 231 | 39% helix, 16% strand | Q91XB0 |
| B | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 234 | 38% helix, 15% strand | Q91XB0 |
| C | A stem loop DNA with Y-structural terminal | dna | 17 | — | — |
| D | A stem loop DNA with Y-structural terminal | dna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.64 | 0.77 | 50 | empty |
| 2 | 505 | 0.63 | 0.76 | 51 | empty |
| 3 | 271 | 0.56 | 0.78 | 17 | empty |
| 4 | 111 | 0.44 | 0.78 | 19 | empty |
| 5 | 81 | 0.33 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1790 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 795 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 771 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 5YWS · Crystal structure of TREX1 in complex with a Y structured DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q91XB0 · AlphaFold monomer V2.0 prediction for three-prime repair exonuclease 1 (Q91XB0) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q91XB0
- Elsewhere: RCSB PDB 5YWS · PDBe 5YWS · UniProt Q91XB0
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